add.missing.F1s	add.missing.F1s
add.slash	add.slash
addLog	addLog
addLogVector	addLogVector
assign.autosome.femaleX.cases	internal_functions
assoc.map	assoc.map
assoc.map.perms	assoc.map
assoc.plot	assoc.plot
assoc.scan1	assoc.scan1
assoc.scan2	assoc.scan2
autosome.femaleX.trans.probs	internal_functions
batch.normalize	normalize.batches
bayesint	bayesint
calc.genoprob	calc.genoprob
calc.genoprob.alleles	calc.genoprob.alleles
calc.genoprob.intensity	calc.genoprob.intensity
categorize.variants	categorize.variants
cc.trans.probs	cc.trans.probs
check.args	internal_functions
chr.skeletons	genome.plots
cluster.strains	cluster.strains
coef.doqtl	coef.doqtl
coefplot	coefplot
colSumsLog	colSumsLog
condense.model.probs	condense.model.probs
convert.allele.calls	convert.allele.calls
convert.genes.to.GRanges	convert.genes.to.GRanges
convert.genotypes	convert.genotypes
convert.pos.to.bp	internal_functions
convert.pos.to.GRanges	internal_functions
convert.variants.to.GRanges	convert.variants.to.GRanges
convert.variants.to.numeric	convert.variants.to.numeric
create.genotype.states	create.genotype.states
create.html.page	create.html.page
create.Rdata.files	create.Rdata.files
do.colors	do.colors
do.states	do.states
do.trans.probs	do.trans.probs
do2sanger	do2sanger
do2sanger.helper	do2sanger
DO_autosome_recomb_freq	internal_functions
DO_femaleX_recomb_freq	internal_functions
DO_maleX_recomb_freq	internal_functions
emission.probs.allele	emission.probs.allele
emission.probs.intensity	emission.probs.allele
emission_prob_from_r	internal_functions
estimate.cluster.params	estimate.cluster.params
example.genes	example.genes
example.pheno	example.pheno
example.qtl	example.qtl
example.snps	example.snps
extract.raw.data	extract.raw.data
fast.qtlrel	fast.qtlrel
femaleX.trans.probs	internal_functions
fill.in.snps	fill.in.snps
filter.geno.probs	filter.geno.probs
filter.samples	filter.samples
filter_smooth_allele	internal_functions
filter_smooth_intensity	internal_functions
find.overlapping.genes	find.overlapping.genes
founder.F1.intensity.plot	intensity.plots
gene.plot	gene.plot
generic.trans.probs	generic.trans.probs
genomic.points	genome.plots
genotype.by.sample.barplot	genome.summary.plots
genotype.by.snp.barplot	genome.summary.plots
get.additive	condense.model.probs
get.chr.lengths	get.chr.lengths
get.do.states	get.do.states
get.dominance	condense.model.probs
get.full	condense.model.probs
get.gene.name	get.gene.name
get.machine.precision	get.machine.precision
get.max.geno	get.max.geno
get.mgi.features	get.mgi.features
get.num.auto	get.num.auto
get.pattern.variants	get.pattern.variants
get.strains	get.strains
get.trans.probs	get.trans.probs
get.variants	get.variants
get.vcf.strains	read.vcf
hmm.allele	hmm
hmm.intensity	hmm
html.report	html.report
initialize.hmm	internal_functions
intensity.mean.covar.plot	intensity.plots
keep.homozygotes	estimate.cluster.params
kinship.alleles	kinship
kinship.probs	kinship
kinship_from_r	internal_functions
maleX.trans.probs	internal_functions
matrixeqtl.snps	scanone.eqtl
muga.snps.to.keep	muga.snps.to.keep
normalize.batches	normalize.batches
num.recomb.plot	summarize.genotype.transitions
parameter.update.alleles	parameter.update
parameter.update.intensity	parameter.update
permutations.qtl.LRS	qtl.LRS
plot.doqtl	plot.doqtl
plot.genoprobs	genome.plots
prsmth.plot	genome.plots
pxg.plot	pxg.plot
qtl.heatmap	qtl.heatmap
qtl.LRS	qtl.LRS
qtl.qtlrel	qtl.qtlrel
qtl.simulate	qtl.simulate
quantilenorm	normalize.batches
rankZ	rankZ
read.vcf	read.vcf
rowSumsLog	colSumsLog
scanone	scanone
scanone.eqtl	scanone.eqtl
scanone.perm	scanone.perm
sdp.plot	sdp.plot
sex.predict	sex.predict
snp.plot	snp.plot
strip.quality.columns	internal_functions
summarize.by.samples	summarize.genotype.transitions
summarize.by.snps	summarize.genotype.transitions
summarize.genotype.transitions	summarize.genotype.transitions
tabulate.geno	internal_functions
update_alleles_from_r	update_from_r
update_from_r	update_from_r
variant.plot	variant.plot
viterbi_from_r	internal_functions
write.founder.genomes	write.founder.genomes
write.genoprob.plots	genome.plots
write.results	write.results
